Gene duplication is considered as the primary source of creating novel materials for genome evolution. It is also associated with many diseases of human genetic disorders. However, previous studies on gene duplication have been biased toward the events that involve the duplication of entire protein-coding genes (e.g., divergence of paralogs). Since duplication break-points arise completely independently of gene boundaries, many small duplication segments may happen within genes, i.e., internal gene fragment duplication. In this proposal, we plan to carry out genome-wide analyses to decipher whether/how gene architectures (e.g., intron birth) are affected duplication events that took place within genes during the evolution process (specific aim 1). In addition, no published studies have investigated the evolutionary process and effects on intergenic DNA regions through population genetics approach. Therefore, we propose to extend our analyses to intergenic DNAs to study their duplication dynamics and fixation process (specific aim 2). Through the proposed global analysis on the duplication processes in internal gene and intergenic region, both of which are poorly understood before, we will provide an unprecedented and unbiased spectrum of genome duplications in eukaryotes. We will carry out the global evolutionary analysis on duplication processes in eukaryotic model organisms with available whole genome sequences. For each organism, we will study the evolutionary demography of internal gene duplications, effects of internal duplication on gene structure variations, and the determinants of the fixation process on duplication products. Through characterization of the duplicated intergenic regions, we propose to identify the sequence with low divergence rate compare to their linked duplication regions as the potential functional elements in intergenic regions. Bioinformatics techniques, population genetics approaches and molecular evolution methods will be applied to achieve above goals. The results will be critical to understand a broad array of unsolved issues in evolutionary genetics, including the extent to which: duplication causes genomic expansion vs. contraction, internal duplication creates immediate changes in structure and function of duplicated genes, and the relative conserved non-coding region under selection, in addition to understanding the mutational basis of genetic disorders caused by duplication,